The fact that the led goes out / comms is lost when you turn on the controller seems to tell me there is a fault loop somewhere.
If you disconnect the UC100 from the board, does the LED stay on?
Disconnect all the inputs/outputs from the board then power up, does the led stay on?
if you can get the pc/m3 communicating ok to the UC/BOB ok, then try connecting just the E-Stop circuit, then test, then gradually build up until it fails.